In this study, the draft genomes of two novel kinds of aerobic denitrifying bacteria, named Agrobacterium sp. LAD9 and Achromobacter sp. GAD3, were reconstructed using Illumina sequencing platforms. Their taxonomic and functional profiles were identified through a series of assembly procedures. Based on the comparison of the performance of simultaneous N and P removal in these two strains, genes encoding enzymes for aerobic denitrification, phosphate and carbon metabolisms were investigated to provide new insight of the metabolisms by aerobic denitrifiers